NBCR's overarching mission is to conduct, catalyze, and enable biomedical research by harnessing forefront computational and information technologies, with a strong focus on translational and multiscale research. In the coming five years we see tremendous opportunities in biomedical research because of the continuing revolution in information technology and the abundance of computing availability. Our objectives are to advance the frontiers of our understanding in multiscale biomedical approaches;provide translational results of significance;accelerate the adoption and development of emerging information technologies by the, biomedical science community;continue to strengthen the multidisciplinarity of the resource;and create multidisciplinary communities of collaborators and users in key areas of translational research. We accomplish these goals through an interrelated set of activities: Integrate computational, data and visualization resources in a transparent way to enable better access to distributed data, computational resources, instruments and people;Develop and deploy advanced computational tools and packages for model building and simulation, three-dimensional image processing, and interactive visualization;Deliver and support advanced cyberinfrastructure tools and environments for biomedical researchers. Train a cadre of new researchers such that they have an interdisciplinary, working knowledge both of experimental biology and of computational technology relevant to biomedical scientists. In this renewal our core technology research and development activities will focus on three themes: 1. Multiscale Model Building and Visualization Tools, for data refinement, visual workflows, mathematical and visual modeling, available in appropriate toolkits and simulation packages. 2. Multiscale Simulation Software Packages and Pipelines for targeted biomedical and translational research to gain those insights into key biomedical processes and diseases, building on NBCR and partner tools and utilizing the cyberinfrastructure. 3. Flexible. Scalable Cvberinfrastructure Framework, to address practical issues of adopting and optimizing some exemplar biomedical applications to the current and emerging cyberinfrastructure while ensuring scientific reproducibility. These developments are driven by collaborative projects on translational research, and have broader impact on the community via service project that use our tools, training on our tools, and dissemination.
Three specific goals of the resource are: Understanding cardiac disease through individual patient modeling;Multiscale modeling at the Mesoscale (between macromolecules and cell);Creating and improving the efficiency of computer aided drug discovery pipeline, with a focus on infectious diseases. Cardiac disease and infectious diseases are leading causes of death in the United States and the world. Filling the gap between the macromolecular and the cellular, at the mesoscale will facilitate the next major developments in computational biology underpinning translational research.
|Kekenes-Huskey, P M; Gillette, A K; McCammon, J A (2014) Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation. J Chem Phys 140:174106|
|Ramachandra, Ranjan; Bouwer, James C; Mackey, Mason R et al. (2014) Improving signal to noise in labeled biological specimens using energy-filtered TEM of sections with a drift correction strategy and a direct detection device. Microsc Microanal 20:706-14|
|Villongco, Christopher T; Krummen, David E; Stark, Paul et al. (2014) Patient-specific modeling of ventricular activation pattern using surface ECG-derived vectorcardiogram in bundle branch block. Prog Biophys Mol Biol 115:305-13|
|Malmstrom, Robert D; Lee, Christopher T; Van Wart, Adam et al. (2014) On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput 10:2648-2657|
|Tangney, Jared R; Campbell, Stuart G; McCulloch, Andrew D et al. (2014) Timing and magnitude of systolic stretch affect myofilament activation and mechanical work. Am J Physiol Heart Circ Physiol 307:H353-60|
|Chen, Eric; Swift, Robert V; Alderson, Nazilla et al. (2014) Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett 5:61-64|
|Pfeiffer, E R; Wright, A T; Edwards, A G et al. (2014) Caveolae in ventricular myocytes are required for stretch-dependent conduction slowing. J Mol Cell Cardiol 76:265-74|
|Gan, Zhuohui; Wang, Jianwu; Salomonis, Nathan et al. (2014) MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. BMC Bioinformatics 15:69|
|Durrant, Jacob D; Amaro, Rommie E (2014) WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinformatics 15:159|
|Demir, Ozlem; Labaied, Mehdi; Merritt, Chris et al. (2014) Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chem Biol Drug Des 84:131-9|
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